SMTL ID : 6ygv.1

tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex with (E)-N-ethyl-4-oxo-4-phenylbut-2-enamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: P.58, E.59, R.62, G.96, W.97, D.98, R.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.58, A:D.98, A:D.98, A:R.99 GOL.2: 8 residues within 4Å: Chain A: Y.108, Q.205, G.231, G.232, L.233, V.235, M.262, G.263 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.232, A:L.233, A:L.233 Water bridges: A:Q.205, A:M.262 GOL.3: 4 residues within 4Å: Chain A: Q.119, S.120, E.121, R.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.121, A:R.176, A:R.176 GOL.4: 7 residues within 4Å: Chain A: L.313, W.328, S.329, C.332 Chain B: L.88, S.93, F.94 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.329, A:S.329, B:S.93, B:F.94 GOL.5: 7 residues within 4Å: Chain A: W.298, E.319, K.362, F.375, D.378, F.379, R.382 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.319, A:K.362, A:D.378 Water bridges: A:E.319, A:R.382 GOL.8: 7 residues within 4Å: Chain B: P.58, E.59, R.62, G.96, W.97, D.98, R.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.58, B:D.98, B:D.98, B:R.99 GOL.9: 8 residues within 4Å: Chain B: Y.108, Q.205, G.231, G.232, L.233, V.235, M.262, G.263 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.232, B:L.233, B:L.233 Water bridges: B:Q.205, B:M.262 GOL.10: 4 residues within 4Å: Chain B: Q.119, S.120, E.121, R.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.121, B:R.176, B:R.176 GOL.11: 7 residues within 4Å: Chain A: L.88, S.93, F.94 Chain B: L.313, W.328, S.329, C.332 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.93, A:F.94, B:S.329, B:S.329 GOL.12: 7 residues within 4Å: Chain B: W.298, E.319, K.362, F.375, D.378, F.379, R.382 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.319, B:K.362, B:D.378 Water bridges: B:R.382

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: C.320, C.322, V.324, C.325, H.351 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.320, A:C.322, A:C.325, A:H.351 ZN.13: 5 residues within 4Å: Chain B: C.320, C.322, V.324, C.325, H.351 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.320, B:C.322, B:C.325, B:H.351

2 x OQH: ~{N}-ethyl-4-oxidanylidene-4-phenyl-butanamide(Covalent)

OQH.7: 13 residues within 4Å: Chain A: W.328, C.332, A.335, L.336, L.343, L.347 Chain B: T.49, K.57, P.58, L.76, P.80, F.94, M.95 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.328, A:A.335, A:L.336, A:L.343, A:L.347, B:L.76, B:F.94 Hydrogen bonds: B:F.94 OQH.14: 13 residues within 4Å: Chain A: T.49, K.57, P.58, L.76, P.80, F.94, M.95 Chain B: W.328, C.332, A.335, L.336, L.343, L.347 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.328, B:A.335, B:L.336, B:L.343, B:L.347, A:L.76, A:F.94 Hydrogen bonds: A:F.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, A. et al., Ligands disturb dimer contacts. To Be Published

Release Date

2020-04-08

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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